Publications by authors named "Andrew F Neuwald"

41Publications

Identifying intracellular signaling modules and exploring pathways associated with breast cancer recurrence.

Sci Rep 2021 Jan 11;11(1):385. Epub 2021 Jan 11.

Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, 900 North Glebe Road, Arlington, VA, 22203, USA.

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January 2021

Author Correction: BICORN: An R package for integrative inference of de novo cis-regulatory modules.

Sci Rep 2020 Oct 7;10(1):16962. Epub 2020 Oct 7.

Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, 900 North Glebe Road, Arlington, VA, 22203, USA.

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October 2020

IntAPT: Integrated assembly of phenotype-specific transcripts from multiple RNA-seq profiles.

Bioinformatics 2020 Oct 5. Epub 2020 Oct 5.

Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA, USA.

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October 2020

Obtaining extremely large and accurate protein multiple sequence alignments from curated hierarchical alignments.

Database (Oxford) 2020 01;2020

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38 A, 8600 Rockville Pike, Bethesda, MD 20894, USA.

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January 2020

BICORN: An R package for integrative inference of de novo cis-regulatory modules.

Sci Rep 2020 05 14;10(1):7960. Epub 2020 May 14.

Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, 900 North Glebe Road, Arlington, VA, 22203, USA.

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May 2020

Deep Analysis of Residue Constraints (DARC): identifying determinants of protein functional specificity.

Sci Rep 2020 02 3;10(1):1691. Epub 2020 Feb 3.

Institute for Genome Sciences and Department of Biochemistry & Molecular Biology, University of Maryland School of Medicine, 670W. Baltimore Steet, Baltimore, MD, 21201, USA.

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February 2020

A survey of TIR domain sequence and structure divergence.

Immunogenetics 2020 04 30;72(3):181-203. Epub 2020 Jan 30.

Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.

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April 2020

Statistical investigations of protein residue direct couplings.

PLoS Comput Biol 2018 12 31;14(12):e1006237. Epub 2018 Dec 31.

Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America.

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December 2018

Inferring joint sequence-structural determinants of protein functional specificity.

Elife 2018 01 16;7. Epub 2018 Jan 16.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States.

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January 2018

Initial Cluster Analysis.

J Comput Biol 2018 02 3;25(2):121-129. Epub 2017 Aug 3.

2 Department of Biochemistry and Molecular Biology, Institute for Genome Sciences, University of Maryland School of Medicine , Baltimore, Maryland.

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February 2018

Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations.

PLoS Comput Biol 2016 12 21;12(12):e1005294. Epub 2016 Dec 21.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States of America.

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December 2016

Bayesian Top-Down Protein Sequence Alignment with Inferred Position-Specific Gap Penalties.

PLoS Comput Biol 2016 05 18;12(5):e1004936. Epub 2016 May 18.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America.

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May 2016

Gleaning structural and functional information from correlations in protein multiple sequence alignments.

Authors:
Andrew F Neuwald

Curr Opin Struct Biol 2016 06 12;38:1-8. Epub 2016 May 12.

Institute for Genome Sciences and Department of Biochemistry & Molecular Biology, University of Maryland School of Medicine, 801 West Baltimore St., BioPark II, Room 617, Baltimore, MD 21201, United States. Electronic address:

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June 2016

Identification and classification of small molecule kinases: insights into substrate recognition and specificity.

BMC Evol Biol 2016 Jan 6;16. Epub 2016 Jan 6.

Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, 30602, USA.

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January 2016

Protein domain hierarchy Gibbs sampling strategies.

Authors:
Andrew F Neuwald

Stat Appl Genet Mol Biol 2014 Aug;13(4):497-517

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August 2014

Evaluating, comparing, and interpreting protein domain hierarchies.

Authors:
Andrew F Neuwald

J Comput Biol 2014 Apr 21;21(4):287-302. Epub 2014 Feb 21.

Institute for Genome Sciences and Department of Biochemistry & Molecular Biology, University of Maryland School of Medicine , Baltimore, Maryland.

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April 2014

A Bayesian sampler for optimization of protein domain hierarchies.

Authors:
Andrew F Neuwald

J Comput Biol 2014 Mar 4;21(3):269-86. Epub 2014 Feb 4.

Institute for Genome Sciences and Department of Biochemistry & Molecular Biology, University of Maryland School of Medicine , Baltimore, Maryland.

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March 2014

Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures.

BMC Bioinformatics 2012 Jun 22;13:144. Epub 2012 Jun 22.

Institute for Genome Sciences and Department of Biochemistry & Molecular Biology, University of Maryland School of Medicine, BioPark II, Room 617, 801 West Baltimore St, Baltimore, MD 21201, USA.

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June 2012

Surveying the manifold divergence of an entire protein class for statistical clues to underlying biochemical mechanisms.

Authors:
Andrew F Neuwald

Stat Appl Genet Mol Biol 2011 4;10:Article 36. Epub 2011 Aug 4.

The University of Maryland, MD, USA.

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May 2012

Bayesian classification of residues associated with protein functional divergence: Arf and Arf-like GTPases.

Authors:
Andrew F Neuwald

Biol Direct 2010 Dec 3;5:66. Epub 2010 Dec 3.

Department of Biochemistry & Molecular Biology, Institute for Genome Sciences, University of Maryland School of Medicine, BioPark II, Room 617, 801 West Baltimore St, Baltimore, MD 21201, USA.

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December 2010

A typhus group-specific protease defies reductive evolution in rickettsiae.

J Bacteriol 2009 Dec 9;191(24):7609-13. Epub 2009 Oct 9.

Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA.

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December 2009

Rapid detection, classification and accurate alignment of up to a million or more related protein sequences.

Authors:
Andrew F Neuwald

Bioinformatics 2009 Aug 8;25(15):1869-75. Epub 2009 Jun 8.

Department of Biochemistry & Molecular Biology and The Institute for Genome Sciences, University of Maryland, School of Medicine, BioPark II, Baltimore, MD 21201, USA.

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August 2009

The charge-dipole pocket: a defining feature of signaling pathway GTPase on/off switches.

Authors:
Andrew F Neuwald

J Mol Biol 2009 Jul 7;390(1):142-53. Epub 2009 May 7.

Institute for Genome Sciences and Department of Biochemistry & Molecular Biology, University of Maryland School of Medicine, Baltimore, 21201, USA.

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July 2009

The glycine brace: a component of Rab, Rho, and Ran GTPases associated with hinge regions of guanine- and phosphate-binding loops.

Authors:
Andrew F Neuwald

BMC Struct Biol 2009 Mar 5;9:11. Epub 2009 Mar 5.

Institute for Genome Sciences and Department of Biochemistry & Molecular Biology, University of Maryland School of Medicine, 801 West Baltimore St,, BioPark II, Baltimore, MD 21201, USA.

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March 2009

Evolution of allostery in the cyclic nucleotide binding module.

Genome Biol 2007 ;8(12):R264

Department of Chemistry and Biochemistry, University of California, Gilman Drive, La Jolla, California 92093-0654, USA.

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March 2008

Analogous regulatory sites within the alphaC-beta4 loop regions of ZAP-70 tyrosine kinase and AGC kinases.

Biochim Biophys Acta 2008 Jan 29;1784(1):27-32. Epub 2007 Sep 29.

Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093-0654, USA.

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January 2008

The CHAIN program: forging evolutionary links to underlying mechanisms.

Authors:
Andrew F Neuwald

Trends Biochem Sci 2007 Nov 24;32(11):487-93. Epub 2007 Oct 24.

The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA.

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November 2007

The hallmark of AGC kinase functional divergence is its C-terminal tail, a cis-acting regulatory module.

Proc Natl Acad Sci U S A 2007 Jan 16;104(4):1272-7. Epub 2007 Jan 16.

Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0654, USA.

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January 2007

Hypothesis: bacterial clamp loader ATPase activation through DNA-dependent repositioning of the catalytic base and of a trans-acting catalytic threonine.

Authors:
Andrew F Neuwald

Nucleic Acids Res 2006 29;34(18):5280-90. Epub 2006 Sep 29.

Cold Spring Harbor Laboratory, 1 Bungtown Road PO Box 100, Cold Spring Harbor, NY 11724, USA.

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December 2006

Bayesian shadows of molecular mechanisms cast in the light of evolution.

Authors:
Andrew F Neuwald

Trends Biochem Sci 2006 Jul;31(7):374-82

Cold Spring Harbor Laboratory, 1 Bungtown Road, PO Box 100, Cold Spring Harbor, NY 11724, USA.

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July 2006

Evolutionary clues to eukaryotic DNA clamp-loading mechanisms: analysis of the functional constraints imposed on replication factor C AAA+ ATPases.

Authors:
Andrew F Neuwald

Nucleic Acids Res 2005 ;33(11):3614-28

Cold Spring Harbor Laboratory, 1 Bungtown Road, PO Box 100, Cold Spring Harbor, NY 11724, USA.

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August 2005

Did protein kinase regulatory mechanisms evolve through elaboration of a simple structural component?

J Mol Biol 2005 Sep;351(5):956-72

Cold Spring Harbor Laboratory, 1 Bungtown Road, P.O. Box 100, Cold Spring Harbor, NY 11724, USA.

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September 2005

Computational analysis of protein tyrosine phosphatases: practical guide to bioinformatics and data resources.

Methods 2005 Jan;35(1):90-114

Cold Spring Harbor Laboratory, Demerec Building, 1 Bungtown Road, Cold Spring Harbor, NY 11724-2208, USA.

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January 2005

Gapped alignment of protein sequence motifs through Monte Carlo optimization of a hidden Markov model.

BMC Bioinformatics 2004 Oct 25;5:157. Epub 2004 Oct 25.

Cold Spring Harbor Laboratory, 1 Bungtown Road, P,O, Box 100, Cold Spring Harbor, NY 11724, USA.

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October 2004

Proteomic analysis of interchromatin granule clusters.

Mol Biol Cell 2004 Aug 28;15(8):3876-90. Epub 2004 May 28.

Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.

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August 2004

Differential contributions of condensin I and condensin II to mitotic chromosome architecture in vertebrate cells.

Cell 2003 Oct;115(1):109-21

Cold Spring Harbor Laboratory, One Bungtown Road, PO Box 100, Cold Spring Harbor, NY 11724, USA.

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October 2003

Evolutionary clues to DNA polymerase III beta clamp structural mechanisms.

Authors:
Andrew F Neuwald

Nucleic Acids Res 2003 Aug;31(15):4503-16

Cold Spring Harbor Laboratory, 1 Bungtown Road, PO Box 100, Cold Spring Harbor, NY 11724, USA.

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August 2003